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Issue 353: Use map to assign prefixes in modifier models #356

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merged 3 commits into from
Jul 9, 2024
Merged

Issue 353: Use map to assign prefixes in modifier models #356

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a892937
fix and test concat bug + generalise to other prefix uses
seabbs Jul 9, 2024
0685b12
fill gap
seabbs Jul 9, 2024
63327be
express it in the samee way eveerywhere
seabbs Jul 9, 2024
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10 changes: 4 additions & 6 deletions EpiAware/src/EpiLatentModels/manipulators/CombineLatentModels.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -31,13 +31,11 @@ latent_model()
P <: AbstractVector{<:String}}
@assert length(models)>1 "At least two models are required"
@assert length(models)==length(prefixes) "The number of models and prefixes must be equal"
for i in eachindex(models)
if (prefixes[i] != "")
models[i] = PrefixLatentModel(models[i], prefixes[i])
end
end
prefix_models = [prefixes[i] == "" ? models[i] :
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PrefixLatentModel(models[i], prefixes[i])
for i in eachindex(models)]
return new{AbstractVector{<:AbstractTuringLatentModel}, AbstractVector{<:String}}(
models, prefixes)
prefix_models, prefixes)
end

function CombineLatentModels(models::M) where {
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10 changes: 4 additions & 6 deletions EpiAware/src/EpiLatentModels/manipulators/ConcatLatentModels.jl
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Expand Up @@ -44,15 +44,13 @@ struct ConcatLatentModels{
@assert typeof(check_dim)<:AbstractVector{Int} "Output of dimension_adaptor must be a vector of integers"
@assert length(check_dim)==no_models "The vector of dimensions must have the same length as the number of models"
@assert length(prefixes)==no_models "The number of models and prefixes must be equal"
for i in eachindex(models)
if (prefixes[i] != "")
models[i] = PrefixLatentModel(models[i], prefixes[i])
end
end
prefix_models = [prefixes[i] == "" ? models[i] :
PrefixLatentModel(models[i], prefixes[i])
for i in eachindex(models)]
return new{
AbstractVector{<:AbstractTuringLatentModel}, Int, Function,
AbstractVector{<:String}}(
models, no_models, dimension_adaptor, prefixes)
prefix_models, no_models, dimension_adaptor, prefixes)
end

function ConcatLatentModels(models::M, dimension_adaptor::Function;
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7 changes: 3 additions & 4 deletions EpiAware/src/EpiObsModels/modifiers/ascertainment/Ascertainment.jl
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Expand Up @@ -30,11 +30,10 @@ struct Ascertainment{
latent_prefix::P) where {
M <: AbstractTuringObservationModel, T <: AbstractTuringLatentModel,
F <: Function, P <: String}
if (latent_prefix != "")
latent_model = PrefixLatentModel(latent_model, latent_prefix)
end
prefix_model = latent_prefix == "" ? latent_model :
PrefixLatentModel(latent_model, latent_prefix)
return new{M, AbstractTuringLatentModel, F, P}(
model, latent_model, link, latent_prefix)
model, prefix_model, link, latent_prefix)
end

function Ascertainment(model::M,
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11 changes: 11 additions & 0 deletions EpiAware/test/EpiLatentModels/manipulators/CombineLatentModels.jl
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Expand Up @@ -16,6 +16,17 @@
@test comb.prefixes == ["Int", "AR"]
end

@testitem "CombineLatentModels constructor handles duplicate models" begin
using Distributions: Normal
comb = CombineLatentModels([Intercept(Normal(0, 1)), Intercept(Normal(0, 2))])
prefix_1 = PrefixLatentModel(Intercept(Normal(0, 1)), "Combine.1")
prefix_2 = PrefixLatentModel(Intercept(Normal(0, 2)), "Combine.2")

@test typeof(comb) <: AbstractTuringLatentModel
@test comb.models == [prefix_1, prefix_2]
@test comb.prefixes == ["Combine.1", "Combine.2"]
end

@testitem "CombineLatentModels generate_latent method works as expected: FixedIntecept + custom" begin
using Turing

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13 changes: 13 additions & 0 deletions EpiAware/test/EpiLatentModels/manipulators/ConcatLatentModels.jl
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Expand Up @@ -32,6 +32,19 @@
@test concat_prefix.prefixes == ["Int", "AR"]
end

@testitem "ConcatLatentmodels constructor works with duplicate models" begin
using Distributions: Normal
concat = ConcatLatentModels([Intercept(Normal(0, 1)), Intercept(Normal(0, 2))])
prefix_1 = PrefixLatentModel(Intercept(Normal(0, 1)), "Concat.1")
prefix_2 = PrefixLatentModel(Intercept(Normal(0, 2)), "Concat.2")

@test typeof(concat) <: AbstractTuringLatentModel
@test concat.models == [prefix_1, prefix_2]
@test concat.no_models == 2
@test concat.dimension_adaptor == equal_dimensions
@test concat.prefixes == ["Concat.1", "Concat.2"]
end

@testitem "ConcatLatentModels generate_latent method works as expected: FixedIntecept + custom" begin
using Turing

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